RMapDB: chemical reaction route map data for quantum mechanical-based data chemistry
Creators
- 1. Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
- 2. Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan
- 3. Software Research Associates Inc., Tokyo 171–8513, Japan
- 4. Department of Media Architecture, Future University Hakodate, Hakodate, Hokkaido 041-8655, Japan
- 5. National Institute of Informatics (NII), Tokyo 101-8430, Japan
- 6. Department of Mathematical Informatics, The University of Tokyo, Tokyo 113-8654, Japan
- 7. Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980–8578, Japan
- 8. Institute for Quantum Chemical Exploration, Konan 1-9-36, Minato-ku, Tokyo 108–0075, Japan
* Contact person
Description
The record contains quantum mechanical (QM) global reaction route map (r-map) data. R-map is chemical reaction pathway networks, which compose equilibrium (EQ) and dissociation channel (DC) and transition state (TS) structures connected via intrinsic reaction coordinates (IRC) obtained by QM calculations. These are contents of RMapDB, which was published first in 2010 as a prototype and has been available online since 2014. The record contains global r-maps of three- to five-atom molecular systems. It contains also a conformational r-map of alpha-D-glucose and a global r-map of C2H4O2, which were discussed in potential energy surface-based conformational analysis and three-dimensional substructure search with the general root mean square deviation (G-RMSD) method. The RMapDB database has been developed in the RMap project for data chemistry based on QM chemical reaction route maps, together with an analytical tool RMapViewer and a server system RMapServer.
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References
Website (Conference proceedings where the database (RMapDB) is described.) H. Satoh, S. Borini, T. Oda, K. Nakakoji, K. Ohno, Global Chemical Reaction Pathway Search with GRRM and Development of Reaction Pathway Library. In proceedings of The New Frontier of Research on The Chemical Reaction Pathways 2012, Tokyo, Japan (2012)
Website (Conference proceedings where the database (RMapDB) is described.) H. Satoh, S. Borini, T. Oda, K. Nakakoji, K. Ohno, Theoretical-Data Chemistry: Data Repository and Applications of Chemical Reaction Path Information Obtained from Scaled Hypersphere Search. Proceedings of Annual Meeting of Japan Society for Molecular Science 2013, Kyoto, Japan, (2013)
Journal reference (Paper in which the database (RMapDB) is described.) H. Satoh, T. Oda, K. Nakakoji, T. Uno, S. Iwata, K. Ohno "Maizo"-chemistry Project: Towards Molecular- and Reaction Discovery from Quantum Mechanical Global Reaction Route Mappings. J. Comput. Chem. Jpn. 14 (3), 77–79 (2015), doi: 10.2477/jccj.2015-0048
Journal reference (Paper in which the data is discussed.) H. Satoh, T. Oda, K. Nakakoji, T. Uno, H. Tanaka, S. Iwata, K. Ohno, Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and its Application on Quantum Mechanical Landscapes of D-Glucose Conformers. J. Chem. Theory Comput., 12, 5293-5308 (2016), doi: 10.1021/acs.jctc.6b00439
Journal reference (Paper in which the data is discussed.) T. Fukutani, K. Miyazawa, S. Iwata, H. Satoh, G-RMSD: Root Mean Square Deviation Based Method for Three-dimensional Molecular Similarity Determination. Bull. Chem. Soc. Jpn. accepted (2020), doi: 10.1246/bcsj.20200258
Website (Webserver where the data can be searched.) H. Satoh, T. Oda, K. Nakakoji, T. Uno, S. Iwata, K. Ohno, Reaction Map Database (2014)
Software (Software to visualize the data.) H. Satoh, T. Oda, K. Nakakoji, T. Uno, S. Iwata, K. Ohno, RMapViewer (2014)
Software (Software to build a database for the data.) H. Satoh, T. Oda, K. Nakakoji, T. Uno, S. Iwata, K. Ohno, Reaction Map Database Server (2018)